Carter 12 - KU ScholarWorks

Paleontological Contributions
Number 12
The paracladistic approach to phylogenetic taxonomy
Joseph G. Carter, Cristian R. Altaba, Laurie C. Anderson, David C. Campbell,
Zongjie Fang, Peter J. Harries, and Peter W. Skelton
April 30, 2015
Lawrence, Kansas, USA
ISSN 1946-0279 (online)
paleo.ku.edu/contributions
Cover illustration: evolutionary hypothesis for the crown group families of superfamily Nuculanoidea (Mollusca, Bivalvia) compatible with
paleontological, anatomical, and molecular data. Exclamation mark (!) indicates that Nuculanidae is paraphyletic.
Paleontological Contributions
April 30, 2015
Number 12
THE PARACLADISTIC APPROACH TO PHYLOGENETIC TAXONOMY
Joseph G. Carter1*, Cristian R. Altaba2, Laurie C. Anderson3, David C. Campbell4,
Zongjie Fang5, Peter J. Harries6, and Peter W. Skelton7
1
Department of Geological Sciences, University of North Carolina, Chapel Hill, NC 27599-3315, USA, e-mail: clams@email.unc.edu;
Human Evolution and Cognition Group (EVOCOG), Universitat de les Illes Balears, 07122, Palma, Balearic Islands, Spain, e-mail: cristianr.altaba@uib.cat; 3South Dakota School of Mines and Technology, Rapid City, SD 57701-3901, USA, e-mail: Laurie.Anderson@sdsmt.
edu; 4Gardner-Webb University, Boiling Springs, NC 28017, USA, e-mail: pleuronaia@gmail.com; 5 State Key Laboratory of Palaeobiology
and Stratigraphy, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing 210008, People’s Republic of China,
e-mail: zjfang@nigpas.ac.cn; 6School of Geosciences, University of South Florida, NES107, Tampa, FL 22620, USA, e-mail: harries@usf.edu;
7
Department of Environment, Earth and Ecosystems, The Open University, Milton Keynes MK7 6AA, United Kingdom,
e-mail: pwskelto@waitrose.com
2
ABSTRACT
The inclusion of some paraphyletic groups in a temporally and taxonomically comprehensive phylogenetic classification
is inevitable because cladistic methodology is incapable of excluding the possibility that a structurally (i.e., based on the
branching pattern of a given cladogram) monophyletic group contains the ancestor of another group, i.e., that it is historically paraphyletic. Paracladistics is proposed as a pragmatic synthesis of phylogenetic and evolutionary taxonomy in which
true monophyly is distinguished from structural monophyly with historical paraphyly, some structurally paraphyletic groups
are retained in the interest of nomenclatorial continuity and stability, and both unranked and suprageneric ranked taxon
names are defined phylogenetically. Ancestral groups are structurally paraphyletic or structurally monophyletic but historically
paraphyletic sets of species that are believed to contain the ancestor for the most recent common ancestor of a descendent
group. Historical paraphyly is determined by considering evidence of nesting in cladistic analyses, timing of first appearances
in the fossil record, polarity in character evolution, and taxa that are morphologically intermediate between groups of species.
The decision to name an ancestral group is based on the same criteria as the decision to name a clade. Ancestral groups are
defined in the same manner as clades, except that their descendent group(s) are designated as external specifiers. Recognizing that two supposedly monophyletic, cladistically defined sister taxa can represent ancestral and descendent groups has
implications for inferring their times of origination. To illustrate the advantages of the paracladistic approach to phylogenetic
taxonomy, alternative paracladistic and phylogenetic classifications of the crown group families of Nuculanoidea (Mollusca,
Bivalvia) are presented.
Keywords: ancestry, cladistics, paracladistics, paraphyly, phylogenetics
INTRODUCTION
Phylogenetic taxonomy, pioneered by Hennig (1950, 1966, 1969),
and with clade nomenclature standardized by the PhyloCode (Cantino
& de Queiroz, 2010), requires all taxa to be monophyletic. The PhyloCode defines monophyly as a set consisting of an ancestor and all
of its descendants. However, phylogenetic taxonomy distinguishes
monophyly solely on the basis of a phylogenetic tree’s branching
pattern as derived from parsimony, likelihood, Bayesian, or other
cladistic analyses of molecular and/or non-molecular data. Further,
phylogenetic tree topology is constrained by the assumption that
sister taxa are monophyletic and originated simultaneously from a
common ancestral species (Altaba, 2009). Non-cladistic evidence to
test whether cladistic sister taxa originated simultaneously, or whether
one cladistic sister taxon contains the ancestor of the other, i.e., that
*Corresponding author.
Copyright © 2015, The University of Kansas, Paleontological Institute
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it might be historically paraphyletic, is excluded from consideration.
Phylogenetic taxonomy maintains its restricted, topological application of the term monophyly by limiting the concept of ancestry to a
definitely identified organism, breeding pair, population, or species
in a monotypic genus. Thus, a group, that is believed to contain the
ancestor for the most recent common ancestor of another group,
is regarded as monophyletic as long as the former ancestor remains
unidentified at the species level. Because species-level ancestry is
virtually impossible to verify, phylogenetic taxonomy effectively
eliminates the concept of ancestry, including the concept of group
ancestry, from taxonomy.
Historical paraphyly can be concealed by a cladistic analysis when
one or more synapomorphies are lost in a descendent group. For
example, the presence of a radula is a synapomorphy in the phylum
Mollusca, but this structure was lost in its class Bivalvia. A cladistic
analysis of the Mollusca might, therefore, resolve the Bivalvia as a
sister group to the remainder of Mollusca. However, paleontological
evidence indicates that the radulate molluscan class Monoplacophora
contains the ancestor of Bivalvia, and is therefore historically paraphyletic with respect to the Bivalvia (Runnegar & Pojeta, 1974;
Carter, Campbell, & Campbell, 2000; Vendrasco, 2012). It is similarly possible for one or more molecular synapomorphies to become
lost or unrecognizable in a descendent group, as exemplified by the
phenomenon of long-branch attraction. Structural monophyly can
also conceal historical paraphyly when a stem group is excluded
from a cladistic analysis. For example, González and Giribet (2014)
concluded, on the basis of molecular phylogenetic evidence, that
the bivalve family Astartidae is monophyletic, yet paleontological
evidence indicates that its extinct subfamily Opinae contains the
ancestor of Crassatellidae (Morris, 1978).
Carter and others (2011) recognized that a truly monophyletic,
temporally and taxonomically comprehensive, phylogenetic classification is unachievable because every truly monophyletic group must
have a corresponding ancestral group, i.e., a structurally paraphyletic
or structurally monophyletic but historically paraphyletic group, that
contains the ancestor for its most recent common ancestor. In their
classification of extant and extinct Bivalvia, they minimized structural
paraphyly by designating paraplesions, i.e., extinct members of a
group that are removed to make the group monophyletic, or to reduce
the extent of paraphyly. However, they retained some structurally
paraphyletic groups in the interest of nomenclatorial continuity and
stability. Carter and others (2012) called this approach to taxonomy
“paracladistic systematics”. It is presently called the paracladistic approach to phylogenetic taxonomy, or just paracladistics.
Paracladistics is presently proposed as a pragmatic synthesis of
phylogenetic and evolutionary taxonomy in which true monophyly
is distinguished from structural monophyly with historical paraphyly,
some structurally paraphyletic groups are retained in the interest
of nomenclatorial continuity and stability, and both unranked and
suprageneric ranked taxon names are defined phylogenetically. To
illustrate the advantages of the paracladistic approach to phylogenetic
taxonomy, alternative paracladistic and phylogenetic classifications
of the crown group families of Nuculanoidea (Mollusca, Bivalvia)
are presented.
Paleontological Contributions, number 12
THE PARACLADISTIC APPROACH
Unlike phylogenetic taxonomy, paracladistics differentiates between true monophyly and structural monophyly with historical
paraphyly. It identifies historical paraphyly by considering nesting in
cladistic analyses, as well as evidence independent of cladistic analyses,
such as timing of first appearances in the fossil record, polarity in
character evolution, and taxa that are believed to be morphologically
transitional between groups of species. Also unlike phylogenetic
taxonomy, paracladistics has the option of retaining widely used,
structurally paraphyletic groups (ancestral groups) in the interest of
nomenclatorial continuity and stability. The paracladistic concept
of ancestral groups is not to be confused with the invalid concept
of group ancestry, if the latter is interpreted to mean that a species
is derived from a group of species rather than from a single species, population, or individual organism (see discussion of ancestry
in phylogenetic taxonomy by Wiley & Lieberman, 2011, p. 241).
Ancestral groups are defined phylogenetically in the same manner
as clades, except that their descendent group(s) are designated as
excluded, external specifiers.
Paracladistics allows for the use of both unranked and rank-based
names, and both descriptive (e.g., Bivalvia) and typified (genericbased) names (e.g., Hominidae). However, other than genera and
species, all taxon names are defined in phylogenetic terms. Rules for
naming rank-based taxa follow the rank-based taxonomic codes, such
as the ICZN (1999) and ICBN (2006), whereas rules for naming
unranked taxa follow the PhyloCode. To maximize compatibility between typified, rank-based names and typified, unranked names, the
PhyloCode convention is adopted that definitions of typified names
include, as an internal specifier, the type species of the nominal genus, and, if it is questionable whether the type species is part of the
group to be named, the genus should not be used as the basis for the
name. Paracladistics strives for concordance between phylogenetic
hierarchy and categorical ranks. However, some discordance might
be unavoidable due to a large number of phylogenetic levels and a
limited number of categorical ranks. Categorical ranks are used merely
as a shorthand indication of inclusivity and degree of morphologic
and/or temporal divergence (Stys & Kerzhner, 1975; Starobogatov,
1991), without other theoretical connotations.
Paracladistics follows the PhyloCode (Article 9.2) convention that
a new clade name derived from a preexisting name must be identified by “converted clade name” or “nomen cladi conversum” (nom.
cl. conv.), whereas a new clade name not derived from a preexisting
name must be identified by “new clade name” or “nomen cladi novum” (nom. cl. nov.). In paracladistics, a new ancestral group name
derived from a preexisting name must be identified by “converted
ancestral group name” or “nomen patrius conversum” (nom. patr. conv.),
whereas a new ancestral group name not derived from a preexisting
name must be identified by “new ancestral group name” or “nomen
patrius novum” (nom. patr. nov.). Ancestral group names are further
identified by an exclamation mark “!” after their name.
For classifications using both unranked and rank-based names,
the PhyloCode recommends placing “[P]” (for phylogenetic) or
“[R]” (for rank-based) after the name, e.g., “Chordata[P]” for an
unranked name as opposed to “Hominidae[R]” for a rank-based
Carter and others—paracladistics
name. Alternatively, one may write “clade Chordata” as opposed
to “family Hominidae” (PhyloCode, Rec. 6.1B). The latter option
is favored for its simplicity, but with the addition of the category
of “ancestral group” for paraphyletic taxa. Widely used, rank-based
typified names of the family-group (subtribe through superfamily)
are preferentially retained as clade or ancestral group names to minimize the proliferation of new names, and to retain the advantages
of the rank-based codes of taxonomic nomenclature. The PhyloCode
recommends that all scientific taxon names should be italicized.
This convention is not presently adopted for all zoological names,
for which the ICZN Code mandates that only genus and species
names should be italicized.
The following phylogenetic and paracladistic classifications of
the crown group families of the superfamily Nuculanoidea illustrate
the advantages of paracladistics when compelling evidence exists for
ancestor-descendant group relationships. Both classifications utilize
the positional number system of Hull (1966), Hennig (1969), and
Ereshefsky (1994) to indicate the phylogenetic hierarchy. By this
method, a taxon’s degree of inclusiveness is indicated by the number
of digits in its identifier: the fewer the digits, the more inclusive
the taxon. As recommended by Wiley and Lieberman (2011, p.
243), the name of an ancestral species is placed on the same line in
the phylogenetic hierarchy as the supraspecific taxon of which its
descendants are parts. Paracladistics applies this convention also to
ancestral group names. Thus, each line in a phylogenetic hierarchy
represents the origination of a clade, ancestral group, and/or ancestral
species. To avoid unintended implications of temporal or phylogenetic
sequence among members of a polytomy, the nominotypical taxon
is listed first, followed by the remaining taxa in alphabetical order.
The superfamily Nuculanoidea contains six extant and two extinct
families (Carter & others, 2011, presently emended). The extinct
family Polidevciidae is presently used as an outgroup to polarize the
evolution of morphological characters for the paracladistic classification. The monogeneric, Jurassic–Paleocene family Isoarcidae Keen,
1969, has no bearing on the present classification and is excluded
from consideration. Morphologic diagnoses for the nuculanoidean
families are summarized below, along with their known geologic
time ranges. These are traditional diagnoses and not lists of synapomorphies. Priority author/date, based on ICZN (1999) rules,
is indicated in parentheses after the nominal family author/date in
cases where these differ:
I. Family Nuculanidae Adams & Adams, 1858 in 1853–1858
(Gray, 1854) (Late Triassic?, Early Jurassic?, Early Cretaceous–Holocene). External ligament weakly mineralized, not prominent; resilium prominent and shallowly to deeply submarginal; hinge teeth
palaeotaxodont; shells porcelaneous, not nacreous; shells generally
posteriorly extended; solid-walled, posterior excurrent siphon well
developed; functional posterior incurrent siphon present; gut not
penetrating deeply into foot; foot lacking strong posterior projection
from its heel; no permanent dorsoposterior shell gape.
II. Family Malletiidae Adams & Adams, 1858 in 1853–1858
(d’Orbigny, 1846 in 1835–1847) (Early Triassic–Holocene). External ligament prominent, strongly mineralized; resilium absent
to small and shallowly to moderately submarginal; hinge teeth
palaeotaxodont; shells porcelaneous, not nacreous; shells generally
3
posteriorly extended; well-developed, solid-walled, posterior excurrent siphon present; functional posterior incurrent siphon present;
gut not penetrating deeply into foot; foot lacking strong posterior
projection from its heel; no permanent dorsoposterior shell gape.
III. Family Phaseolidae Scarlato & Starobogatov, 1971 (Pliocene–Holocene). External ligament greatly reduced; resilium deeply
submarginal and internal; hinge teeth partially to entirely imbricate
lamellar; shells porcelaneous, not nacreous; shells slightly posteriorly
extended; well-developed, solid-walled, posterior excurrent siphon
present; functional posterior incurrent siphon present; gut not penetrating deeply into foot; foot with strong posterior projection from
its heel; shells not gaping or permanently gaping dorsoposteriorly.
IV. Family Polidevciidae Kumpera, Prantl, & Růžička, 1960
(Ordovician–Late Jurassic). External ligament prominent, strongly
mineralized; resilium small to moderately well developed, shallowly
to deeply submarginal; hinge teeth palaeotaxodont; shells nacreous,
not porcelaneous; shells posteriorly extended; posterior excurrent
siphon absent or minimally developed, based on absence of a pallial
sinus; presence or absence of functional posterior incurrent siphon
unknown; anatomy of gut and foot unknown; no permanent dorsoposterior shell gape.
V. Family Siliculidae Allen & Sanders, 1973 (Late Cretaceous–Holocene). External ligament greatly reduced, resilium deeply
submarginal to slightly internal; hinge teeth rarely entirely palaeotaxodont, more commonly transitional palaeotaxodont/imbricate
lamellar or entirely imbricate lamellar; shells porcelaneous, not nacreous; shells slightly to greatly posteriorly extended; well-developed,
solid-walled, posterior excurrent siphon present; functional posterior
incurrent siphon absent; gut penetrating deeply into foot; foot lacking strong posterior projection from its heel; shells not gaping or
permanently gaping dorsoposteriorly.
VI. Family Tindariidae Verrill & Bush, 1897 (Late Cretaceous–Holocene). External ligament prominent, well mineralized;
resilium absent to minute and shallowly submarginal; hinge teeth
palaeotaxodont; shells porcelaneous, not nacreous; posterior part of
shell extended or reduced; posterior, excurrent siphon well-developed
to reduced; functional posterior incurrent siphon absent or present; gut penetrating deeply into foot; foot lacking strong posterior
projection from its heel; no permanent dorsoposterior shell gape.
VII. Family Zealedidae Scarlato & Starobogatov, 1979 (Paleocene–Holocene). External ligament reduced, non-mineralized; resilium small, shallowly submerged; hinge teeth palaeotaxodont; shells
porcelaneous, not nacreous; shells posteriorly slightly to moderately
extended; posterior, excurrent siphon present, with hollow walls;
functional posterior incurrent siphon present; gut not penetrating
deeply into foot; foot lacking strong posterior projection from its
heel; no permanent dorsoposterior shell gape.
The alternative phylogenetic and paracladistic classifications utilize
three molecular phylogenetic analyses for the subclass Protobranchia
from Sharma and others (2013). The Nuculanoidea portion of one of
these analyses (maximum-parsimony based on direct optimization) is
reproduced in Figure 1, with colors added to highlight the distribution of the traditional families. The other two molecular phylogenetic
analyses, based on maximum likelihood and Bayesian inference, are
not presently illustrated. They both differ from Figure 1 in resolving
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Paleontological Contributions, number 12
Figure 1. Parsimony analysis under direct optimization of five genes (numbers on nodes indicate jackknife resampling frequencies (>50%, with ‘*’
indicating 100%) for the Nuculanoidea, one of four molecular phylogenetic topologies in Sharma and others (2013: fig. 4). Colors indicate family assignment prior to the present taxonomic revision and correspond to the color coding applied to the family names. Note that the species of Jupiteria is
now assigned to the genus Nuculana.
the Zealedidae and Malletiidae as monophyletic, in resolving the
Tindariidae as polyphyletic, and in placing the sareptoidean family
Pristiglomidae within the clade of Nuculanoidea. Pristiglomidae
does not appear in Figure 1 because in this molecular phylogenetic
analysis it was resolved as a sister group to Nuculanoidea. All three
molecular phylogenetic analyses resolved the family Nuculanidae as
paraphyletic, and populated its members across two clades. One clade
also contains the Malletiidae and most or all Tindariidae; the other
clade also contains the Zealedidae, Siliculidae, Phaseolidae, and, in
the two molecular analyses not presently illustrated, the tindariid
Clencharia abyssorum (Verrill & Bush, 1898).
We begin the phylogenetic classification by naming the two major
clades in Figure 1 the Malletiiformes and Nuculaniformes (Fig. 2).
Neither clade corresponds to a traditional taxonomic grouping, nor
has an apparent morphological synapomorphy. Within the Malletiiformes, subclades Malletiidae and Tindariidae, both also lacking an
apparent morphological synapomorphy, can be defined as monophyletic groups on the basis of at least one of the three molecular
phylogenetic analyses. The Nuculaniformes shows two subclades,
one smaller and one much larger, in all three molecular phylogenetic
analyses. However, all three molecular analyses place Nuculana pella
(Linnaeus, 1767) in the smaller subclade, apart from other members
of its genus, and two of the molecular analyses (not Fig. 1) resolve
the tindariid Clencharia abyssorum in the smaller subclade rather
than with other members of Tindariidae in the Malletiiformes. We
choose not to name these two Nuculaniformes subclades because of
their variable taxonomic composition and because neither subclade
would have an apparent morphological synapomorphy.
The clade Nuculaniformes contains all analyzed members of the
families Zealedidae, Phaseolidae, and Siliculidae, as well as most
of the Nuculanidae, including Nuculana pernula (O. F. Müller,
1779), the type species for its genus. The Zealedidae was resolved
as monophyletic in two of the three molecular phylogenetic analyses
(not Figure 1). Its hollow siphon walls provide the grounds for an
apomorphy-based clade definition. The Phaseolidae was represented
in the molecular phylogenetic analyses by only one species, Lametila
abyssorum Allen and Sanders, 1973. However, a clade Phaseolidae can
be defined on the basis of this species and Phaseolus ovatus Monterosato, 1875, the type species for its nominal genus. The Siliculidae
was resolved as paraphyletic in all three molecular phylogenetic
analyses, and it has no apparent morphological synapomorphies.
Siliculidae cannot presently be restricted to a monopyletic subset of
Carter and others—paracladistics
5
Figure 2. Same as Figure 1, but with the superimposed phylogenetic classification. Clades Malletiiformes and Nuculaniformes each contain two families
plus several traditional members of the Nuculanidae, or Nuculanidae and Siliculidae, respectively, that are not assigned to a family.
its traditional members because the type species of Silicula was not
included in the molecular phylogenetic analyses, so its phylogenetic
position relative to the analyzed siliculids is unknown (PhyloCode
Recommendation 11.7A). We elect not to restrict the family Nuculanidae to the small clade of Nuculana pernula, Nuculana conceptionis
(Dall, 1896), Nuculana minuta (O. F. Müller, 1776), and Jupiteria
sematensis (Suzuki & Ishizuka, 1943) (= Nuculana according to World
Register of Marine Species, 2015), because such restriction would
limit Nuculanidae to a subset of the genus Nuculana.
The present phylogenetic classification of Nuculanoidea is illustrated in Figure 2 and summarized below, using the positional number
system to indicate phylogenetic hierarchy. The classification follows
the PhyloCode convention of listing after a clade name the nominal
author/date followed, in square brackets “[ ]”, by the definitional
author/date. The nominal author/date indicates the first publication of a taxon name with the spelling adopted as the clade name,
regardless whether it was phylogenetically defined. The definitional
author/date indicates the first publication of a phylogenetic definition for a name, either the original definition or an emended one.
As required by the PhyloCode, definitions of clade names converted
from typified names include the type species of the nominal genus
as an internal specifier. Note that the clade Malletiiformes contains
four traditional members of Nuculanidae, not assigned to a subclade.
Also, the clade Nuculaniformes contains several traditional members
of Nuculanidae and all traditional members of Siliculidae, also not
assigned to a subclade.
1. Clade Malletiiformes [nom. cl. nov.]. The most recent common ancestor of Malletia cuneata (Jeffreys, 1876), Malletia chilensis
Des Moulins, 1832 (the type species of Malletia), and Tindaria kennerlyi (Dall, 1897) that is not also an ancestor of Nuculana pernula
(O. F. Müller, 1779), plus all descendants of that common ancestor.
1.1. Clade Malletiidae Nevesskaja & others, 1971. [nom. cl.
conv.]. The clade originating with the most recent common ancestor of Malletia cuneata (Jeffreys, 1876) and Malletia chilensis Des
Moulins, 1832 (the type species of Malletia).
1.2. Clade Tindariidae Scarlato and Starobogatov, 1971 [nom.
cl. conv.]. The clade originating with the most recent common
ancestor of Tindaria kennerlyi (Dall, 1897), Tindaria arata Bellardi,
1875 (the type species of Tindaria), and Clencharia abyssorum (Verrill & Bush, 1898).
2. Clade Nuculaniformes [nom. clad. nov.]. The most recent
common ancestor of Nuculana pernula (O. F. Müller, 1779) (the type
species of Nuculana) that is not also an ancestor of Malletia cuneata
(Jeffreys, 1876), plus all descendants of that common ancestor.
2.1. Clade Phaseolidae Scarlato & Starobogatov, 1971 [nom.
cl. conv.]. The most recent common ancestor of Phaseolus ovatus
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Monterosato, 1875 (the type species of Phaseolus) and Lametila abyssorum Allen & Sanders, 1973, that is not also an ancestor of Yoldiella
americana Allen, Sanders & Hannah, 1995, plus all descendants of
that common ancestor.
2.2. Family Zealedidae Scarlato & Starobogatov, 1979 [nom.
cl. conv.]. The clade originating with the first species to possess hollow siphon walls as inherited by Ledella pustulosa (Jeffreys, 1876),
Bathyspinula hilleri (Allen & Sanders, 1982), and Zealeda hamata
Marwick, 1924 (the type species of Zealeda).
We turn now to the paracladistic classification of crown group
Nuculanoidea. The paracladistic classification differs from the
phylogenetic alternative in retaining the family Nuculanidae as a
paraphyletic, ancestral group, thereby making the names Malletiiformes and Nuculaniformes obsolete. All three molecular phylogenetic analyses resolved some members of Nuculanidae basal to
all members of Malletiidae, Tindariidae, Zealedidae, Phaseolidae,
and Siliculidae. This is compatible with the hypothesis that Nuculanidae contains the direct or indirect ancestor(s) for these five
groups. The most ancient nuculanoidean family, the Polidevciidae,
is characterized by nacreous (mother-of-pearl) shells, non-gaping,
dorsoposterior shell margins, and palaeotaxodont hinge teeth, i.e.,
chevron-like hinge teeth with non-lamellar shapes. In contrast, all
extant nuculanoideans have non-nacreous, porcelaneous shells. Of
the extant nuculanoidean families with only palaeotaxodont hinge
teeth, the Nuculanidae and Malletiidae appeared first in the fossil
record. The Malletiidae might have predated the Nuculanidae, but
this is uncertain. Both families were present by the Early Cretaceous,
before all other extant nuculanoidean families. However, nuculanid
and malletiid shells are externally similar, and the two families are
differentiated largely on the basis of ligament structure, which is
poorly known for many early Mesozoic putative members. Until
the first appearance of Nuculanidae is better known, and until more
molecular data become available for Malletiidae, we tentatively accept
the molecular phylogenetic evidence that Nuculanidae contains the
ancestor of Malletiidae. The Nuculanidae can therefore be defined
as the ancestral group originating with the first species to possess
porcelaneous, non-nacreous shells, as inherited by Nuculana pernula (O. F. Müller, 1779) (the type species of Nuculana), with the
exclusion of its directly or indirectly descendent families, which are
designated as external specifiers.
Malletiidae and Tindariidae both resemble Polidevciidae and
differ from Nuculanidae in having a prominent, external ligament,
and the molecular evidence suggests that Malletiidae and Tindariidae
are very closely related. However, a Malletiidae + Tindariidae clade
would have no apparent morphological synapomorphies, and the
molecular evidence does not justify excluding traditional nuculanids
from such a clade. These two families are therefore inferred to have
been derived independently from separate ancestors in Nuculanidae. The molecular phylogenetic evidence is also compatible with
the hypothesis that Nuculanidae is directly ancestral to Zealedidae,
which was resolved as monophyletic in two of the three molecular
phylogenetic analyses (but not in Fig. 1).
None of the molecular phylogenetic analyses resolved the grouping
Siliculidae + Phaseolidae as monophyletic, but one analysis (Fig. 1)
placed the one analyzed phaseolid, Lametila abyssorum, in an adjacent
Paleontological Contributions, number 12
position to Siliculidae. Most members of Siliculidae and all members
of Phaseolidae differ from all the other nuculanoidean families in
replacing the plesiomorphic palaeotaxodont hinge teeth with at least
partially imbricate lamellar hinge teeth, and most members of both
families also have a distinctive, permanent, dorsoposterior shell gape.
The siliculid Propeleda Iredale, 1924, resembles many nuculanids in
its posteriorly elongate, rostrate shell shape, submarginal, non-internal
ligamental resilium, distinct commarginal sculpture, and single, faint,
anterior radial rib in each valve. Further, Propeleda louiseae (Clarke,
1961) has transitional palaeotaxodont/imbricate lamellar hinge teeth
(Allen & Sanders, 1996, fig. 43). Phaseolids are more derived than
siliculids in terms of their more internally positioned resilium and
presence of a functional, posterior incurrent siphon. These features,
and the earlier appearance of Siliculidae than Phaseolidae in the fossil record, suggest that Siliculidae was derived from an ancestor in
Nuculanidae, and that it contains the ancestor of Phaseolidae. This
inference can be represented in the paracladistic classification by
emending the family Phaseolidae to contain the basal, paraphyletic
subfamily Siliculinae and its descendent subfamily Phaseolinae.
The use of Phaseolidae (instead of Siliculidae) for the family name
is required by priority and the ICZN principle of coordination of
family-group names.
In the following summary of the paracladistic classification, Siliculinae is placed at the same level in the phylogenetic hierarchy as its
family Phaseolidae because they represent the same origination event.
The paraphyletic nature of Nuculanidae and Siliculinae is indicated
by the exclamation mark after their name. As in the phylogenetic
classification, clade names that are converted from typified names
include, as an internal specifier, the type species of the nominal
genus. Authorship and dates of publication conform to ICZN rules
because, in this classification, all clade and ancestral group names are
typified, family-group names. Priority author/date for family-group
names is indicated in parentheses “( )” after the nominal author/date
in cases where these differ. Note that the paracladistic classification
preserves all of the traditional nuculanoidean families except for
Siliculidae, which is reduced in rank to a subfamily of Phaseolidae.
1. Family Nuculanidae! Adams & Adams, 1858 in 1853–1858
(Gray, 1854). The ancestral group originating with the first species to
possess porcelaneous, non-nacreous shells, as inherited by Nuculana
pernula (O. F. Müller, 1779) (the type species of Nuculana), excluding the descendent families Tindariidae, Malletiidae, Zealedidae,
and Siliculidae.
1.1. Family Malletiidae Adams & Adams, 1858 in 1853–1858
(d’Orbigny, 1846 in 1835–1847). The clade originating with the
most recent common ancestor of Malletia cuneata (Jeffreys, 1876) and
Malletia chilensis Des Moulins, 1832 (the type species of Malletia).
1.2. Family Phaseolidae Scarlato, & Starobogatov, 1971.
The clade originating with the most recent common ancestor of
Phaseolus ovatus Monterosato, 1875 (the type species of Phaseolus),
Lametila abyssorum Allen & Sanders, 1973, Silicula fragilis Jeffreys,
1879 (the type species of Silicula), and Propeleda louiseae (Clarke,
1961). Subfamily Siliculinae! Allen & Sanders, 1973. The clade
originating with the most recent common ancestor of Silicula fragilis
Jeffreys, 1879 (the type species of Silicula), and Propeleda louiseae
(Clarke, 1961), excluding the descendent subfamily Phaseolinae.
7
Carter and others—paracladistics
1.2.1. Subfamily Phaseolinae Scarlato & Starobogatov, 1971.
The clade originating with the most recent common ancestor of
Phaseolus ovatus Monterosato, 1875 (the type species of Phaseolus)
and Lametila abyssorum Allen & Sanders, 1973.
1.3. Family Tindariidae Verrill & Bush, 1897. The clade
originating with the most recent common ancestor of Tindaria
kennerlyi (Dall, 1897), Tindaria arata Bellardi, 1875 (the type species of Tindaria), and Clencharia abyssorum (Verrill & Bush, 1898).
1.4. Family Zealedidae Scarlato & Starobogatov, 1979. The
clade originating with the first species to possess hollow siphon walls,
as inherited by Ledella pustulosa (Jeffreys, 1876), Bathyspinula hilleri
(Allen & Sanders, 1982), and Zealeda hamata Marwick, 1924 (the
type species of Zealeda).
DISCUSSION
It is the goal of phylogenetic taxonomy to discover and diagnose
monophyletic groups, yet its cladistic methodology is incapable of
distinguishing between true monophyly and structural monophyly
with historical paraphyly. Further, the inclusion of some historically
paraphyletic groups is unavoidable in any temporally and taxonomically comprehensive phylogenetic classification. The paracladistic
approach differs from the strictly phylogenetic approach in distinguishing between true monophyly and structural monophyly with
historical paraphyly, and in accepting some widely used, structurally paraphyletic groups. These differences promote nomenclatorial
stability as well as continuity with traditional taxonomy, while also
adding an evolutionary dimension to phylogenetic taxonomy. The
decision to name a structurally paraphyletic group is based on the
same criteria as those for naming a clade. According to the PhyloCode,
these include, but are not restricted to, level of support, phenotypic
distinctiveness, economic importance, and whether the clade (or in
this case paraphyletic group) has historically been named.
Dias, Assis, and Udulutsch (2005) have argued that accepting
[structurally] paraphyletic groups will result in taxonomic chaos, or
groups that contain no phylogenetic information. To the contrary, the
present paracladistic classification of the Nuculanoidea demonstrates
that structurally paraphyletic groups, such as the Nuculanidae, can be
phylogenetically defined with the same rigor as clades, and that they
can convey useful phylogenetic and evolutionary information. The
paracladistic classification is compatible with the molecular phylogenetic data in Sharma and others (2013), except for its recognition
of a Siliculidae + Phaseolidae clade, based on non-cladistic evidence.
Recognizing the difference between true monophyly and structural
monophyly with historical paraphyly has implications for inferring
time of origination of cladistically defined sister taxa. For example,
molecular phylogenetic analyses of extant bivalves resolve the order
Unionida as a sister group to the order Trigoniida, thereby implying a ghost lineage for Unionida of about 130 Ma (Bieler & others,
2014, fig. S2; Gonzales & Giribet, 2014, fig. 3; Gonzales & others,
2015, fig. 2). The morphological phylogenetic analysis of extant and
extinct bivalves by Carter, Campbell, and Campbell (2006) resolved
the Unionida as a sister group to the Trigoniida family Trigonodidae,
implying a ghost lineage for Unionida of 5–10 Ma. In contrast,
non-cladistic, paleontological evidence suggests that both inferences of timing are incorrect, and that Unionida was derived from
a contemporaneous, Late Triassic member of Trigonodidae (Newell
& Boyd, 1975, p. 136; Carter, Campbell & Campbell, 2006). In a
second example, phylogenetic taxonomy regards the sister subtribes
Hominina Gray, 1825, and Australopithecina Gregory and Hellman,
1939, as derived simultaneously from a most recent common ancestor 3.9 – 4.2 million years ago (Haviland & others, 2008, p. 134).
This contradicts paleontological evidence that Hominina dates from
only about 2.8 million years ago (Villmoare & others, 2015). From
the paracladistic perspective, Hominina was derived either from a
most recent common ancestor with Australopithecina, or from one
of its members (Cela-Conde & Altaba, 2002; Cela-Conde & Ayala,
2003). These examples illustrate that the paracladistic approach to
phylogenetic taxonomy can be more heuristic and evolutionarily
more accurate than strictly cladistic phylogenetics.
ACKNOWLEDGMENTS
We thank Philip D. Cantino, Michel Laurin, Nikolaus Malchus,
David Marjanovic, and Kevin de Queiroz for their comments on
early drafts of this paper. We are also grateful to Abby Hooker for
steering us toward data pertinent to the discussion.
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